What is the difference between Cosine and Modified Cosine similarity?

Standard Cosine similarity matches peaks directly, while Modified Cosine accounts for differences in precursor m/z, making it more effective for identifying related molecules.

How does this skill improve Claude's ability to handle scientific data?

It provides Claude with specific Python implementation patterns and best practices for mass spectrometry, ensuring code for spectral analysis is accurate and efficient.

Can I use this skill to calculate chemical structure similarity?

Yes, Matchms includes capabilities to derive InChI and SMILES, add fingerprints (like Morgan), and calculate FingerprintSimilarity between compounds.

What mass spectrometry file formats are supported?

Matchms supports a wide range of formats including mzML, mzXML, MGF (Mascot Generic Format), MSP, and GNPS-compatible JSON.

Does Matchms help with metadata cleaning?

Absolutely. It features over 40 filters to harmonize compound names, correct adducts, standardize charges, and derive structural information.

Matchms Mass Spectrometry Analysis

Name: Matchms Mass Spectrometry Analysis
Author: BbgnsurfTech

byBbgnsurfTech

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数据科学与机器学习

Processes, filters, and analyzes mass spectrometry data using Python-based spectral similarity and metadata harmonization.

Matchms is a specialized Claude Code skill designed for researchers and data scientists working with metabolomics and mass spectrometry. It enables Claude to assist in importing complex data formats like mzML, MGF, or MSP, applying over 40 metadata and peak filters, and calculating advanced spectral similarities such as Modified Cosine. Whether you are matching unknown spectra against reference libraries, cleaning raw spectral data, or building reproducible analytical pipelines, this skill provides the domain-specific logic and implementation patterns required for professional-grade mass spectrometry workflows.

主要功能

01Advanced similarity metrics including CosineGreedy and Modified Cosine

02Molecular structure derivation and fingerprinting (SMILES/InChI)

033 GitHub stars

04Multi-format support for mzML, MGF, MSP, and JSON spectral data

05Standardized pipelines for reproducible spectrum processing

0640+ built-in filters for metadata harmonization and peak refinement

使用场景

01Automating metadata standardization for large-scale chemical databases

02Identifying unknown compounds by matching queries against spectral libraries

03Preprocessing and cleaning raw mass spectrometry data for metabolomics

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add bbgnsurftech/claude-skills-collection matchms

For use in Claude.ai and ChatGPT

Download Skill